But, plotting does not work for MS2 chrom and spec

In the last couple of commits, the application has become much more
reactive. I have focused on throwing out as many as possible important
observers in favour of render/reactive environments.

As a consequence, the application is much more responsive to change
and updates properly almost all the time.

It used to be that the control got stuck when adding and removing tags
in the tag input box which is now fixed. This is not a _minor_ thing,
although it sounds like it. From now on, the user should not be
confronted with unexpected behaviour.

* change the extraction system from mzr to MSnbase
* change the plotting subsystem from base graphics to ggplot2